AMBER Archive (2003)

Subject: Re: Calcium in proteins

From: David A. Case (case_at_scripps.edu)
Date: Tue May 20 2003 - 09:40:06 CDT

On Mon, May 19, 2003, Javier Cuervo wrote:
>
> How can I deal with proteins that has Calcium ions (Ca2+), It seems to me
> that some forcefield (amber99) has parameters for it (C0), but I have not
> been able to produce a .top or .crd files using leap.
>

(1) You don't say what things you tried, and what happened as a result.

(2) Basially, you have to create a UNIT in LEaP that gives you what you
want. This might be a bare calcium ion (for that, see examples in
$AMBERHOME/dat/leap/lib/ions94.cmd, and create Ca2+ in an analogous way);
or, you might want a hydrated ion, treating the calcium and its first
solvation shell waters as a "molecule". An example of this is here:

%A V. Tsui
%A D.A. Case
%T Calculations of the Absolute Free Energies of Binding between RNA and Metal
%Ions Using Molecular Dynamics Simulations and Continuum Electrostatics
%J J. Phys. Chem. B
%V 105
%P 11314-11325
%D 2001

(3) Note that simulating divalent ions is *not* a standard piece of molecular
mechanics repertoire, which is partially why there are no pre-defined
residues. You might want to look at this:

%A T. Dudev
%A C. Lim
%T Principles Governing Mg, Ca, and Zn Binding and Selectivity in Proteins
%J Chem. Rev.
%V 103
%P 773-788
%D 2003

..good luck...dac 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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